Contacts of the helix formed by residues 53 - 66 (chain A) in PDB entry 1MJP
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A LEU* 4.5 4.9 - - - +
36A LEU* 3.6 26.3 - - + +
37A THR* 3.1 36.2 + - - -
40A ARG* 2.9 39.4 - - - +
52A THR* 1.3 67.5 - - - +
54A SER* 1.3 72.3 + - - +
56A LEU* 2.8 16.8 + - - +
57A LEU* 2.9 17.4 + - + +
24B ILE* 5.5 6.4 - - + +
2D G 2.9 14.1 + - - +
3D A 5.2 6.1 + - - -
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Residues in contact with SER 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A THR* 4.0 3.6 - - - -
53A ASN* 1.3 76.0 - - - +
55A GLU* 1.3 63.8 + - - +
57A LEU* 2.9 5.7 + - - +
58A CYS* 2.9 26.1 + - - -
25B THR 4.0 1.2 + - - -
26B VAL* 3.4 19.2 - - - +
27B SER* 3.0 47.6 + - - -
1D A 3.9 6.1 - - - -
2D G 2.6 27.3 + - - -
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PRO* 4.8 0.8 - - - +
11A TYR* 3.1 37.7 - - + +
17A LYS* 5.6 6.5 + - - -
50A HIS* 2.7 54.9 + - + -
51A ALA 3.5 1.7 + - - -
52A THR* 3.2 24.5 + - - +
53A ASN 3.2 0.2 - - - -
54A SER* 1.3 79.2 - - - +
56A LEU* 1.3 68.8 + - - +
58A CYS* 3.3 8.1 + - - +
59A GLU* 2.9 26.9 + - - +
1D A 6.5 0.7 - - - -
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 3.8 24.2 - - + +
39A GLU* 3.3 32.5 - - + +
40A ARG* 3.8 23.8 - - + +
43A ARG* 3.0 48.0 - - - +
52A THR 3.0 10.5 + - - +
53A ASN* 2.8 15.1 + - - +
55A GLU* 1.3 77.7 - - - +
57A LEU* 1.3 63.8 + - - +
59A GLU* 3.0 18.9 - - - +
60A ALA* 3.0 8.0 + - - +
61B PHE* 5.4 4.7 - - + -
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 4.9 3.8 - - + -
28A ILE* 6.2 1.8 - - + -
36A LEU* 3.7 31.4 - - + -
53A ASN* 2.9 14.1 + - + +
54A SER* 2.9 7.1 + - - +
56A LEU* 1.3 71.6 - - - +
58A CYS* 1.3 69.8 + - - +
60A ALA* 2.7 20.7 + - - +
61A PHE* 3.1 12.4 + - - +
24B ILE* 4.3 13.0 - - + -
26B VAL* 3.9 35.4 - - + -
57B LEU* 5.2 23.8 - - + -
61B PHE* 4.4 16.6 - - + -
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Residues in contact with CYS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PRO* 3.7 25.8 - - + +
54A SER* 2.9 20.1 + - - -
55A GLU* 3.8 6.3 - - - +
57A LEU* 1.3 75.3 - - - +
59A GLU* 1.3 63.4 + - - +
61A PHE* 3.7 8.0 - - - +
62A LEU* 3.5 25.8 + - - +
26B VAL* 4.8 4.0 - - - -
27B SER 3.6 22.9 - - - -
28B ILE* 3.7 23.3 - - - -
29B PRO* 4.0 7.2 - - + -
32B VAL* 4.9 7.7 - - + +
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A PRO* 3.7 24.0 - - + -
11A TYR* 2.6 30.3 + - + +
43A ARG* 2.6 45.0 + - - -
50A HIS* 3.8 2.4 - - - +
55A GLU 2.9 14.6 + - - +
56A LEU* 3.0 12.4 - - - +
57A LEU 2.8 3.8 + - - -
58A CYS* 1.3 73.4 - - - +
60A ALA* 1.3 67.5 + - - +
62A LEU* 3.6 4.1 + - - +
63A HIS* 3.2 19.1 + - - +
70A LEU* 4.0 12.9 - - + +
71A PRO* 4.2 16.2 - - + +
76A LEU* 4.5 0.2 - - - +
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Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU 3.0 7.0 + - - +
57A LEU* 2.7 16.8 + - - +
59A GLU* 1.3 71.4 - - - +
61A PHE* 1.3 72.5 + - - +
63A HIS* 3.0 7.4 + - - +
64A ALA* 3.0 18.9 + - - +
70A LEU* 4.7 2.2 - - - +
60B ALA* 3.9 5.8 - - + +
61B PHE* 3.5 38.6 - - + +
64B ALA* 3.9 14.0 - - + +
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Residues in contact with PHE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A LEU 3.1 6.3 + - - +
58A CYS* 3.7 11.4 - - - +
60A ALA* 1.3 86.7 - - - +
62A LEU* 1.3 74.9 + - + +
63A HIS 2.5 0.3 + - - -
64A ALA* 2.8 10.2 + - + -
65A PHE* 2.9 36.4 + + + -
32B VAL* 4.1 22.9 - - + -
35B ILE* 3.9 18.2 - - + -
36B LEU* 3.1 65.3 - - + -
39B GLU* 5.2 4.5 - - + -
56B LEU* 5.3 6.5 - - + -
57B LEU* 5.1 8.7 - - + -
60B ALA* 3.8 19.3 - - + +
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 3.6 35.0 - - + +
9A SER 4.2 2.0 - - - -
10A PRO* 3.6 43.3 - - + -
58A CYS 3.5 9.3 + - - +
59A GLU* 3.6 7.9 - - - +
61A PHE* 1.3 87.8 - - + +
63A HIS* 1.3 51.2 + - - +
65A PHE* 4.7 3.6 - - + -
66A THR* 2.3 60.1 + - + +
68A GLN* 3.7 17.9 - - + +
32B VAL* 4.2 15.5 - - + -
35B ILE* 5.7 6.3 - - + -
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Residues in contact with HIS 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLU 3.2 2.2 + - - +
60A ALA 3.0 8.0 + - - +
61A PHE 2.5 4.8 + - - -
62A LEU* 1.3 74.7 - - - +
64A ALA* 1.3 69.9 + - - +
67A GLY* 2.3 54.9 + - - +
68A GLN* 2.3 36.6 + - + +
69A PRO* 4.0 7.2 - - + +
70A LEU* 3.5 40.3 - - + +
63B HIS* 3.8 25.2 + + - -
64B ALA* 4.4 6.2 + - + -
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ALA 3.0 5.8 + - - +
61A PHE* 2.8 9.6 + - - +
63A HIS* 1.3 79.5 - - - +
65A PHE* 1.3 57.8 + - - +
66A THR 5.0 0.2 - - - -
67A GLY* 4.5 1.6 + - - -
60B ALA* 4.2 13.5 - - + +
63B HIS* 3.2 34.1 - - + -
70B LEU* 3.4 30.9 - - + +
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Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A PHE* 2.9 43.5 + + + +
62A LEU* 4.0 2.9 - - + +
64A ALA* 1.3 79.1 - - - +
66A THR* 1.3 74.0 + - + +
35B ILE* 3.6 30.5 - - + -
39B GLU* 3.7 40.8 - - + -
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Residues in contact with THR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A GLU 3.4 13.9 - - - +
3A TRP* 3.3 22.7 - - - -
4A SER 4.7 0.5 + - - -
6A GLU 5.7 0.4 - - - -
8A ILE* 5.3 5.6 - - + -
62A LEU* 2.3 52.0 + - + +
65A PHE* 1.3 96.0 - - + +
67A GLY* 1.3 56.2 + - - +
68A GLN* 3.2 20.5 + - - +
35B ILE* 5.8 4.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il